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Persistent homology

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https://www.readbyqxmd.com/read/28100608/herpes-simplex-virus-type-1-ul24-abrogates-dna-sensing-signal-pathway-by-inhibiting-nf-%C3%AE%C2%BAb-activation
#1
Haiyan Xu, Chenhe Su, Angela Pearson, Christopher H Mody, Chunfu Zheng
: Cyclic GMP-AMP synthase (cGAS) is a newly identified DNA sensor that recognizes foreign DNA, including the genome of herpes simplex virus 1 (HSV-1). Upon binding of viral DNA, cGAS produces cyclic GMP-AMP, which interacts with and activates stimulator of interferon genes (STING) to trigger the transcription of anti-viral genes such as type I interferons and production of inflammatory cytokines. HSV-1 UL24 is widely conserved among the herpesviruses family and is essential for efficient viral replication...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28056965/phylogenetic-characterization-of-genes-encoding-for-viral-envelope-glycoprotein-orf5-and-nucleocapsid-protein-orf7-of-porcine-reproductive-respiratory-syndrome-virus-found-in-malaysia-in-2013-and-2014
#2
Seetha Jaganathan King, Peck Toung Ooi, Lai Yee Phang, Zeenathul Nazariah Binti Allaudin, Wei Hoong Loh, Chiou Yan Tee, Shiao Pau How, Lai Siong Yip, Pow Yoon Choo, Ban Keong Lim
BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is one of the most expensive diseases of modern swine production & results in annual economic losses and cost the industry over 600 million USD in U.S. alone and billions of dollars worldwide. Two atypical PRRS cases were observed in 2013 and 2014 characterized by late-term abortion, fever and sudden increase in sow mortality which persisted for a prolonged period of time. METHODS: Lungs, lymph nodes and other samples were collected for disease investigation...
January 5, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28052350/eses-software-for-eulerian-solvent-excluded-surface
#3
Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong, Guo-Wei Wei
Solvent excluded surface (SES) is one of the most popular surface definitions in biophysics and molecular biology. In addition to its usage in biomolecular visualization, it has been widely used in implicit solvent models, in which SES is usually immersed in a Cartesian mesh. Therefore, it is important to construct SESs in the Eulerian representation for biophysical modeling and computation. This work describes a software package called Eulerian solvent excluded surface (ESES) for the generation of accurate SESs in Cartesian grids...
January 4, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28049740/resolvase-osgen1-mediates-dna-repair-by-homologous-recombination
#4
Chong Wang, James Higgins, Yi He, Pingli Lu, Dabing Zhang, Wanqi Liang
Yen1/GEN1 are canonical Holliday Junction (HJ) resolvases that belong to the RAD2/XPG family. In eukaryotes, such as budding yeast, mice, worms, and humans, Yen1/GEN1 work together with Mus81-Mms4/MUS81-EME1 and Slx1-Slx4/SLX1-SLX4 in DNA repair by homologous recombination to maintain genome stability. In plants, the biological function of Yen1/GEN1 remains largely unclear. In this study, we characterized the loss of function mutants of OsGEN1 and OsSEND1, a pair of paralogs of Yen1/GEN1 in rice. We first investigated the role of OsGEN1 during meiosis and found a reduction in chiasma frequency by ~6% in osgen1 mutants, compared to wild type, suggesting a possible involvement of OsGEN1 in the formation of crossovers...
January 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28046127/structure-function-network-mapping-and-its-assessment-via-persistent-homology
#5
Hualou Liang, Hongbin Wang
Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28046077/an-oxygen-sensing-two-component-system-in-the-burkholderia-cepacia-complex-regulates-biofilm-intracellular-invasion-and-pathogenicity
#6
Matthew M Schaefers, Tiffany L Liao, Nicole M Boisvert, Damien Roux, Deborah Yoder-Himes, Gregory P Priebe
Burkholderia dolosa is a member of the Burkholderia cepacia complex (BCC), which is a group of bacteria that cause chronic lung infection in patients with cystic fibrosis (CF) and can be associated with outbreaks carrying high morbidity and mortality. While investigating the genomic diversity of B. dolosa strains collected from an outbreak among CF patients, we previously identified fixL as a gene showing signs of strong positive selection. This gene has homology to fixL of the rhizobial FixL/FixJ two-component system...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28039075/comparative-genome-analysis-of-multiple-vancomycin-resistant-enterococcus-faecium-isolated-from-two-fatal-cases
#7
Shu Yong Lim, Kien-Pong Yap, Cindy Shuan Ju Teh, Kartini Abdul Jabar, Kwai Lin Thong
Enterococcus faecium is both a commensal of the human intestinal tract and an opportunistic pathogen. The increasing incidence of enterococcal infections is mainly due to the ability of this organism to develop resistance to multiple antibiotics, including vancomycin. The aim of this study was to perform comparative genome analyses on four vancomycin-resistant Enterococcus faecium (VREfm) strains isolated from two fatal cases in a tertiary hospital in Malaysia. Two sequence types, ST80 and ST203, were identified which belong to the clinically important clonal complex (CC) 17...
December 28, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28017642/immunity-duration-of-a-recombinant-adenovirus-type-5-vector-based-ebola-vaccine-and-a-homologous-prime-boost-immunisation-in-healthy-adults-in-china-final-report-of-a-randomised-double-blind-placebo-controlled-phase-1-trial
#8
Jing-Xin Li, Li-Hua Hou, Fan-Yue Meng, Shi-Po Wu, Yue-Mei Hu, Qi Liang, Kai Chu, Zhe Zhang, Jun-Jie Xu, Rong Tang, Wen-Juan Wang, Pei Liu, Jia-Lei Hu, Li Luo, Rong Jiang, Feng-Cai Zhu, Wei Chen
BACKGROUND: The 2013-15 Ebola virus disease epidemic in west Africa greatly accelerated the development of Ebola vaccine. We aimed to analyse the immune persistence induced by one shot of an adenovirus type-5 vector-based Ebola virus vaccine up to 6 months and the effect of boosting with a homologous vector in healthy adults in China. METHODS: In a randomised, double-blind, placebo-controlled, phase 1 clinical trial in one site in Jiangsu Province, China, 120 healthy adults aged 18-60 years received an initial dose of intramuscular adenovirus type-5 Ebola virus vaccine of 4·0 × 10(10) viral particles, 1·6 × 10(11) viral particles, or placebo, and were followed up to day 168...
December 22, 2016: Lancet Global Health
https://www.readbyqxmd.com/read/28017426/viral-vector-vaccines-protect-cockatiels-from-inflammatory-lesions-after-heterologous-parrot-bornavirus-2-challenge-infection
#9
Solveig Runge, Marita Olbert, Christiane Herden, Sara Malberg, Angela Römer-Oberdörfer, Peter Staeheli, Dennis Rubbenstroth
Avian bornaviruses are causative agents of proventricular dilatation disease (PDD), a chronic neurologic and often fatal disorder of psittacines including endangered species. To date no causative therapy or immunoprophylaxis is available. Our previous work has shown that viral vector vaccines can delay the course of homologous bornavirus challenge infections but failed to protect against PDD when persistent infection was not prevented. The goal of this study was to refine our avian bornavirus vaccination and infection model to better represent natural bornavirus infections in order to achieve full protection against a heterologous challenge infection...
December 22, 2016: Vaccine
https://www.readbyqxmd.com/read/28007925/long-term-maintenance-of-the-influenza-specific-cross-reactive-memory-cd4-t-cell-responses-following-repeated-annual-influenza-vaccination
#10
Mai-Chi Trieu, Fan Zhou, Sarah Lartey, Åsne Jul-Larsen, Siri Mjaaland, Saranya Sridhar, Rebecca Jane Cox
BACKGROUND: Annual vaccination for healthcare workers and other high-risk groups is the mainstay of the public health strategy to combat influenza. Inactivated influenza vaccines confer protection by inducing neutralizing antibodies efficiently against homologous and closely-matched virus strains. In the absence of neutralizing antibodies, cross-reactive T-cells have been shown to limit disease severity. However, animal studies and a study in immunocompromised children suggested that repeated vaccination hampers the CD8(+) T-cells...
December 22, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27999619/comparative-genomics-analyses-revealed-two-virulent-listeria-monocytogenes-strains-isolated-from-ready-to-eat-food
#11
Shu Yong Lim, Kien-Pong Yap, Kwai Lin Thong
BACKGROUND: Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. RESULTS: The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively...
2016: Gut Pathogens
https://www.readbyqxmd.com/read/27986806/repair-of-meiotic-dna-breaks-and-homolog-pairing-in-mouse-meiosis-requires-a-minichromosome-maintenance-mcm-paralog
#12
Adrian J McNairn, Vera D Rinaldi, John C Schimenti
The mammalian Mcm-domain containing 2 (Mcmdc2) gene encodes a protein of unknown function that is homologous to the mini-chromosome maintenance family of DNA replication licensing and helicase factors. Drosophila melanogaster contains two separate genes, the "Mei-MCMs," that appear to have arisen from a single ancestral Mcmdc2 gene. The Mei-MCMs are involved in promoting meiotic crossovers by blocking the anti-crossover activity of BLM helicase, a function presumably performed by MSH4 and MSH5 in metazoans...
December 16, 2016: Genetics
https://www.readbyqxmd.com/read/27974687/the-effects-of-ppri-gene-of-deinococcus-radiodurans-r1-on-acute-radiation-injury-of-mice-exposed-to-60co-%C3%AE-ray-radiation
#13
Ting-Ting Chen, Wei Hua, Xi-Zhi Zhang, Bu-Hai Wang, Zhan-Shan Yang
The role of the pprI gene from Deinococcus radiodurans R1 in therapy of acute radiation injury of a mammalian host was investigated. We injected a plasmid containing the pprI gene into the muscle of mice exposed to total 6Gy of 60Co γ-ray radiation. After injection, we used in vivo gene electroporation technology to transfer the pprI gene into the cell. We found the PprI protein was expressed significantly at 1 d after irradiation, but there was no expression of pprI gene 7 d post-irradiation. The expression of pprI gene evidently decreased the death rate of mice exposed to lethal dose radiation, significantly relieved effects on blood cells in the acute stage, shortened the persistence time of the decrease of lymphocytes, and decreased the apoptotic rates of spleen cells, thymocytes and bone marrow cells...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27956220/physiologically-based-pharmacokinetic-toolkit-to-evaluate-environmental-exposures-applications-of-the-dioxin-model-to-study-real-life-exposures
#14
Claude Emond, Patricia Ruiz, Moiz Mumtaz
Chlorinated dibenzo-p-dioxins (CDDs) are a series of mono- to octa-chlorinated homologous chemicals commonly referred to as polychlorinated dioxins. One of the most potent, well-known, and persistent member of this family is 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). As part of translational research to make computerized models accessible to health risk assessors, we present a Berkeley Madonna recoded version of the human physiologically based pharmacokinetic (PBPK) model used by the U.S. Environmental Protection Agency (EPA) in the recent dioxin assessment...
December 10, 2016: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/27930309/sox2-progenitors-in-sharks-link-taste-development-with-the-evolution-of-regenerative-teeth-from-denticles
#15
Kyle J Martin, Liam J Rasch, Rory L Cooper, Brian D Metscher, Zerina Johanson, Gareth J Fraser
Teeth and denticles belong to a specialized class of mineralizing epithelial appendages called odontodes. Although homology of oral teeth in jawed vertebrates is well supported, the evolutionary origin of teeth and their relationship with other odontode types is less clear. We compared the cellular and molecular mechanisms directing development of teeth and skin denticles in sharks, where both odontode types are retained. We show that teeth and denticles are deeply homologous developmental modules with equivalent underlying odontode gene regulatory networks (GRNs)...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911727/role-of-the-bone-morphogenic-protein-pathway-in-developmental-haemopoiesis-and-leukaemogenesis
#16
REVIEW
Parto Toofan, Helen Wheadon
Myeloid leukaemias share the common characteristics of being stem cell-derived clonal diseases, characterised by excessive proliferation of one or more myeloid lineage. Chronic myeloid leukaemia (CML) arises from a genetic alteration in a normal haemopoietic stem cell (HSC) giving rise to a leukaemic stem cell (LSC) within the bone marrow (BM) 'niche'. CML is characterised by the presence of the oncogenic tyrosine kinase fusion protein breakpoint cluster region-abelson murine leukaemia viral oncogene homolog 1 (BCR-ABL), which is responsible for driving the disease through activation of downstream signal transduction pathways...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27902438/dna-double-strand-break-repair-is-involved-in-desiccation-resistance-of-sinorhizobium-meliloti-but-is-not-essential-for-its-symbiotic-interaction-with-medicago-truncatula
#17
Pierre Dupuy, Benjamin Gourion, Laurent Sauviac, Claude Bruand
The soil bacterium Sinorhizobium meliloti, a nitrogen-fixing symbiont of legume plants, is exposed to numerous stress conditions in nature, some of which cause the formation of harmful DNA double strand breaks (DSB). In particular, the reactive oxygen (ROS) and nitrogen (RNS) species produced during symbiosis, and the desiccation occurring in dry soils, are conditions which induce DSB. Two major systems of DSB repair are known in S. meliloti: homologous recombination (HR) and non-homologous end-joining (NHEJ)...
November 23, 2016: Microbiology
https://www.readbyqxmd.com/read/27896283/a-potential-founder-variant-in-carmil2-rltpr-in-three-norwegian-families-with-warts-molluscum-contagiosum-and-t-cell-dysfunction
#18
Hanne S Sorte, Liv T Osnes, Børre Fevang, Pål Aukrust, Hans C Erichsen, Paul H Backe, Tore G Abrahamsen, Ole B Kittang, Torstein Øverland, Shalini N Jhangiani, Donna M Muzny, Magnus D Vigeland, Pubudu Samarakoon, Tomasz Gambin, Zeynep H C Akdemir, Richard A Gibbs, Olaug K Rødningen, Robert Lyle, James R Lupski, Asbjørg Stray-Pedersen
BACKGROUND: Four patients from three Norwegian families presented with a common skin phenotype of warts, molluscum contagiosum, and dermatitis since early childhood, and various other immunological features. Warts are a common manifestation of human papilloma virus (HPV), but when they are overwhelming, disseminated and/or persistent, and presenting together with other immunological features, a primary immunodeficiency disease (PIDD) may be suspected. METHODS AND RESULTS: The four patients were exome sequenced as part of a larger study for detecting genetic causes of primary immunodeficiencies...
November 2016: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/27895125/lineage-specific-soxr-mediated-regulation-of-an-endoribonuclease-protects-non-enteric-bacteria-from-redox-active-compounds
#19
Jisun Kim, Chulwoo Park, James A Imlay, Woojun Park
Bacteria use redox-sensitive transcription factors to coordinate responses to redox stress. The [2Fe-2S] cluster-containing transcription factor SoxR is particularly tuned to protect cells against redox-active compounds (RACs). In enteric bacteria, SoxR is paired with a second transcription factor, SoxS, that activates downstream effectors. However, SoxS is absent in non-enteric bacteria, raising questions as to how SoxR functions. Here, we first show that SoxR of Acinetobacter oleivorans displayed similar activation profiles in response to RACs as did its homolog from Escherichia coli but controlled a different set of target genes, including sinE, which encodes an endoribonuclease...
January 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27881779/allergic-inflammation-leads-to-neuropathic-pain-via-glial-cell-activation
#20
Ryo Yamasaki, Takayuki Fujii, Bing Wang, Katsuhisa Masaki, Mizuho A Kido, Mari Yoshida, Takuya Matsushita, Jun-Ichi Kira
: Allergic and atopic disorders have increased over the past few decades and have been associated with neuropsychiatric conditions, such as autism spectrum disorder and asthmatic amyotrophy. Myelitis presenting with neuropathic pain can occur in patients with atopic disorder; however, the relationship between allergic inflammation and neuropathic pain, and the underlying mechanism, remains to be established. We studied whether allergic inflammation affects the spinal nociceptive system...
November 23, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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